The alternate routes are interesting, but lack enough benefit to be a rational choice. ten extra days of training is not a fair trade for potential achievement progress. Giving you a small permanent bonus (perhaps an achievement in itself) would go a long way to increase it's usefulness
As one of few people who consistently plays past loop 15, I agree, but with reservations. The goal is that long-term, a player that skips loops should end up about as strong as a player that doesn't. The intended way to balance this is with item strength, and I'd agree with you that currently the items don't give enough to make the playing field level by loop 20 or so (I'd estimate the crossover point somewhere around Loop 25, which is out past the current end of content). But the gap is actually quite narrow, because items over the long term do matter a lot more than Forsaken. Over the long term, achievements will hit their maximum level in time, and over the long term, players will get much more Forsaken than are useful or even convenient to keep. If items are priced correctly both players will have teams of highly specialized Forsaken that have earned all relevant achievements at some point in the twenties. I think a buff would really throw it out of whack in favor of players that skip loops.
What I'd previously suggested was gating the three "pick another item from this list of three" items behind alternate routes, as well as a fourth item that lets players pick between another choice of starting items. I still say that giving alternate routes a choice between items would balance it out a bit more. Players who want to skip past Loop 4 do not get an actual item choice in Loop 3--they must take the Loop with a Superior Chosen whatever the item there is. Players who skip past Loop 4 do not have much time to train their Superior Forsaken to be strong enough to achieve a Distortion against the Animalistic in Loop 5, limiting their choice there to the Undead. So the first time this player may have a real choice in items is Loop 7. Currently to take the Loop 11 alternate route, players also give up their boss choice in Loop 10 (I assume another skip will be implemented once Angels are in). This combined with an early dearth in Forsaken means that these playthroughs don't have as many interesting, consequential decisions as a player who fights in every loop--some item variety would change this.